dynein-cell-model

Dependencies

System Packages (Required)

Install these before building:

Ubuntu/Debian:

sudo apt update
sudo apt install -y libopencv-dev libhdf5-dev

macOS (Homebrew):

brew install opencv hdf5

Finding HDF5 Paths (macOS)

If CMake can't find HDF5 automatically, you may need to specify the paths:

# Find HDF5 paths
brew --prefix hdf5
# Example output: /opt/homebrew/opt/hdf5

# Find the cmake config directory
ls /opt/homebrew/opt/hdf5/lib/cmake/
# Example output: hdf5-1.14.6

Then configure with:

mkdir build && cd build
cmake .. -DHDF5_DIR=/opt/homebrew/opt/hdf5/lib/cmake/hdf5-1.14.6
cmake --build . -j4

Build

# Create build directory
mkdir build && cd build

# Configure (uses FetchContent for most dependencies)
cmake ..

# Build
cmake --build . -j4

Optional: OpenMP (for parallelization)

OpenMP is auto-detected. On Linux with GCC, it will be enabled automatically.

macOS: OpenMP requires GCC (not Clang). To enable:

brew install gcc
export CC=/opt/homebrew/bin/gcc-15
export CXX=/opt/homebrew/bin/g++-15
cmake ..

Linux: Install GCC if not present:

sudo apt install build-essential

Quick Start

# After building
./build/examples/run_model_metrics <config_file>

Testing

# Run tests
cd build && ctest

Project Structure

• src/dynein_cell_model/ - Main cell model library
• examples/ - Example executables
• scripts/ - Python analysis scripts
• cmake/ - CMake configuration files